refactor: update logging to always output to STDOUT/STDERR by default

IFTPipeline.jl/src/cli.jl

@@ -1,7 +1,6 @@
 #!/usr/bin/env julia
 
 using ArgParse
-using LoggingExtras
 using IceFloeTracker
 using IFTPipeline
 using Serialization
@@ -228,34 +227,6 @@ function mkcli!(settings, common_args)
 end
 
 
-"""
-    setuplogger(option::Int64, path::String)
-
-Setup logger for the ice floe tracker. If `option` is 0, log to file only. If `option` is 1, log to file and terminal.
-"""
-function setuplogger(option::Int64, command::Symbol)
-    output = joinpath(@__DIR__, "..", "report")
-    cmd = string(command)
-
-    filelogger = FileLogger(joinpath(output, "$cmd-logfile.log")) # add command prefix to logfile name
-
-    # filter out debug messages
-    filtlogger = EarlyFilteredLogger(filelogger) do args
-        r = Logging.Info <= args.level <= Logging.Warn && args._module === IFTPipeline
-        return r
-    end
-
-    if option == 0
-        return TeeLogger(filtlogger,
-        )
-    elseif option == 1
-        return TeeLogger(
-            global_logger(),
-            filtlogger
-        )
-    end
-end
-
 function main()
 
     settings = ArgParseSettings(; autofix_names=true)
@@ -281,12 +252,9 @@ function main()
         help = "Pair ice floes in day k with ice floes in day k+1"
         action = :command
     end
-
-    command_common_args = [
-        "--log",
-        Dict(:help => "Show log on terminal; either 1 or 0", :required => false, :arg_type => Int,
-            :default => 0, :range_tester => (x -> x == 0 || x == 1)
-        )]
+
+    command_common_args = []
+
 
     mkcli!(settings, command_common_args)
 
@@ -295,16 +263,11 @@ function main()
     command = parsed_args[:_COMMAND_]
     command_args = parsed_args[command]
     command_func = getfield(IFTPipeline, Symbol(command))
-    logoption = command_args[:log]
 
-    # delete log option from command_args so it doesn't get passed to command_func
-    delete!(command_args, :log)
-
-    logger = setuplogger(logoption, command)
-
-    with_logger(logger) do
-        @time command_func(; command_args...)
-    end
+    @debug "debug message"
+    @info "info message"
+    @time command_func(; command_args...)
+
     return nothing
 end
 

IFTPipeline.jl/test/_test-cli.sh

@@ -0,0 +1,25 @@
+#!/usr/bin/env bash
+
+# Scripts
+IFT="julia --project=../ ../src/cli.jl"
+
+# Data source and target
+DATA_SOURCE=test_inputs/input_pipeline
+TEMPDIR=$(mktemp -d -p __temp__)
+echo "TEMPDIR=${TEMPDIR}"
+
+# Initialize data directory
+cp ${DATA_SOURCE}/20220914.{terra,aqua}.{true,false}color.250m.tiff ${TEMPDIR}
+cp ${DATA_SOURCE}/landmask.tiff ${TEMPDIR}
+cp ${DATA_SOURCE}/passtimes_lat.csv ${TEMPDIR}
+SAMPLEIMG=${TEMPDIR}/20220914.terra.truecolor.250m.tiff
+
+# Set up debug messages
+export JULIA_DEBUG="Main,IFTPipeline,IceFloeTracker" 
+
+# Run the processing
+${IFT} landmask ${TEMPDIR} ${TEMPDIR}
+${IFT} preprocess -t ${TEMPDIR} -r ${TEMPDIR} -l ${TEMPDIR} -p ${TEMPDIR} -o ${TEMPDIR}
+${IFT} extractfeatures -i ${TEMPDIR} -o ${TEMPDIR}
+${IFT} track --imgs ${TEMPDIR} --props ${TEMPDIR} --passtimes ${TEMPDIR} --latlon ${SAMPLEIMG} -o ${TEMPDIR}
+${IFT} makeh5files --pathtosampleimg ${SAMPLEIMG} --resdir ${TEMPDIR}

README.md

@@ -280,3 +280,38 @@ ift_segmented = np.ma.masked_array(ift_segmented, mask=ift_segmented==0)
 fig, ax = plt.subplots()
 ax.imshow(ift_segmented, cmap='prism')
 ```
+
+## Logging
+
+The command line tools all implement logging to `Stderr`.
+
+To redirect Stdout and Stderr  to a file, append `&> outfile.log` to the command, e.g.:
+```bash
+julia --project=IFTPipeline.jl IFTPipeline.jl/src/cli.jl landmask ./input_directory/ ./output_directory/ &> outfile.log
+```
+
+To print the output to the console in addition to writing it to a file, append  `|& tee outfile.log` to the command, e.g.:
+```bash
+julia --project=IFTPipeline.jl IFTPipeline.jl/src/cli.jl landmask ./input_directory/ ./output_directory/ |& tee outfile.log
+```
+
+This works the same way for all the command line tools, including those in Julia, Python, and Bash.
+
+When used within the cylc workflow, the logs are automatically saved to the `cylc-run` directory 
+and can be viewed using the `cylc tui` or `cylc gui` or viewed directly from the terminal, e.g.:
+```bash
+cat ./cylc-run/<workflow-name>/<run#>/log/job/1/<task-name>/01/job.err
+```
+
+Debug messages (from `@debug` macros in the code) can be activated for 
+each command line task by calling Julia with the `JULIA_DEBUG` environment variable set.
+
+To activate debug logging for the Ice Floe Tracker, call:
+```bash
+JULIA_DEBUG="Main,IFTPipeline,IceFloeTracker" julia --project=IFTPipeline.jl IFTPipeline.jl/src/cli.jl landmask
+```
+
+To activate debug logging for all the packages used (many more messages), call:
+```bash
+JULIA_DEBUG="all" julia --project=IFTPipeline.jl IFTPipeline.jl/src/cli.jl landmask ...
+```